People in York are preparing for the River Ouse to peak nearly five metres above normal on Thursday morning.
The fire service is pumping water from some riverside homes and businesses.
The Environment Agency said it did not expect the river level to breach flood defences but said it sympathised with residents of homes not protected.
A spokesman said there were concerns for the Cawood and Selby areas which will see river levels swell on Thursday as rain water goes downstream.
Craig McGarvey, from the agency, said the River Ouse would peak at about 08:00 BST on York. It has risen by more than 13ft (4m) since Sunday.
Mr McGarvey said: “it is going to rise a little bit more but it isn’t going to go over the top of the defences.
“Obviously some people are undefended in York and obviously our sympathies go to them.”
He said the agency was monitoring the situation in Cawood and Selby with the police and local authority.
“We think the water at Cawood will go very close to the top of the defences, Mr McGarvey said.
“If we can reduce the risk of flooding we will.”
The town of Tadcaster has been split in two after flooding forced the closure of a major road bridge over the River Wharfe.
The Mayor of Tadcaster, Steve Cobb, said the Wharfe was at its highest level since major floods hit the area in 2000.
He said a number of businesses close to the river had been flooded.
“We’re one community but we are split in two today,” Mr Cobb said.
“We are totally dependent on the bridge. It’s a four or five mile trip around without it, just to get to the other side.
“We have a doctor’s on one side, schools on both sides, all sorts of businesses on either side. We’ve got our fingers crossed. We’ve got everything crossed.”
The county council said engineers were checking the bridge, which carries the A659 over the River Wharfe.
A spokeswoman added a full inspection would not be possible until river levels subsided.
The bridge over the River Ure in Boroughbridge has also been closed and nearby residents had to be rescued by the fire service.
More than 20 residents from a retirement complex had to be rescued by North Yorkshire Fire and Rescue after they were cut-off by flood water.
Residents at Minerva Court had been without power since Tuesday evening. They were taken to temporary accommodation.
A couple also had to be rescued by the fire service after becoming stranded in a boat on the river.
Residents from 20 homes at Dalton, near Thirsk, were also rescued from their homes.
Oliver Harmar, from the Environment Agency, said: “We have had unprecedented levels of rainfall which is now feeding its way through the system.
“Our latest forecasts is showing that levels will only exceed riverside footpaths and a small band of riverside properties.”
Defences in York are 18ft (5.5m) high and the Environment Agency predicts the level of the river will reach 16ft (4.9m) at its highest level.
Linda Barker and her husband, Michael, have been stranded on their boat in the middle of the Ouse at York.
She said: “We managed to get to the York Boat pontoon yesterday and moor up. We are completely stranded and can’t get off the boat. Hopefully the river will peak today but it will take a few days to drop and we don’t really know what to expect.
“The boat is our home so I wouldn’t want to leave though.”
The transport network across North Yorkshire has been badly affected by flooding, North Yorkshire Police said.
Assistant Chief Constable of North Yorkshire Ian Spittal, said: “The areas of roads that have bridges that have been closed they all need to be checked structurally before they are reopened.
“That is going to take some time. So the number of roads that are disrupted at the moment will continue for at least the next 24 to 48 hours until those checks are done.”
Mr Spittal said the force was working closely with the Environment Agency and its main focus was in the York and Selby areas where river levels were yet to peak.
A 40-mile section of the A1(M) in the county has reopened southbound after being closed for more than 24 hours.
The Highways Agency said it could not say when the northbound carriageway would be reopened.